Publications - Research Paper

2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2003 |

2002 | 1997 |


2017 top

Gearing up to handle the mosaic nature of life in the quest for orthologs

Forslund, K.; Pereira, C.; Capella-Gutierrez, S.; Sousa da Silva, A.; Altenhoff, A.; Huerta-Cepas, J.; Muffato, M.; Patricio, M.; Vandepoele, K.; Ebersberger, I.; Blake, J.; Breis, J.T.F.

the Quest for Orthologs Consortium: Boeckmann, B.; Gabaldón, T.; Sonnhammer, E.; Dessimoz, C.; Lewis, S.

Bioinformatics 2017 Aug 30. doi: 10.1093/bioinformatics/btx542. [Epub ahead of print]


Natural product diversity associated with the nematode symbionts Photorhabdus and Xenorhabdus

Tobias, N.;  Wolff, H.;  Djahanschiri, B.;  Grundmann, F.;  Kronenwerth, M.;  Shi, Y.;  Simonyi, S.;  Grün, P.;  Shapiro-Ilan, D.;  Pidot, S.;  Stinear, T.;  Ebersberger, I.;  Bode, H.

Nat Microbiol. 2017 Oct 9. doi: 10.1038/s41564-017-0039-9. [Epub ahead of print]


The draft genome of blunt snout bream (Megalobrama amblycephala) reveals the development of intermuscular bone and adaptation to herbivorous diet.

Liu, H.; Chen, C.; Gao, Z.; Min, J.; Gu, Y.; Jian, J.; Jiang, X.; Cai, H.; Ebersberger, I.; Xu, M.; Zhang, X.; Chen, J.; Luo, W.; Chen, B.; Chen, J.; Liu, H.; Li, J.; Lai, R.; Bai, M.; Wei, J.; Yi, S.; Wang, H.; Cao, X.; Zhou, X.; Zhao, Y.; Wei, K.; Yang, R.; Liu, B.; Zhao, S.; Fang, X.; Schartl, M.; Qian, X.; Wang, W.

Gigascience. 2017 May 23. doi: 10.1093/gigascience/gix039. [Epub ahead of print]


An annotated draft genome for Radix auricularia (Gastropoda, Mollusca)

Schell, T.; Feldmeyer, B.; Schmidt, H.; Greshake, B.; Tills, O.; Truebano, M.; Rundle, SD.; Paule, J.; Ebersberger, I.; Pfenninger, M.;

Genome Biol Evol. 2017 Feb 15. doi: 10.1093/gbe/evx032. [Epub ahead of print]


2016 top

Characterization of microsatellite loci in the lichen-forming fungus Cetraria aculeata (Parmeliaceae, Ascomycota).

Lutsak, T.; Fernández-Mendoza, F.; Greshake, B.; Dal Grande, F.; Ebersberger, I.; Ott, S.; Printzen, C.

Appl Plant Sci. 2016 Sep 19;4(9). pii: apps.1600047. doi: 10.3732/apps.1600047.


An evolutionary perspective of AMPK-TOR signaling in the three domains of life

Roustan, V.; Jain, A.; Teige, M.; Ebersberger, I.; Weckwerth, W.;

Exp Bot. 2016 Jun;67(13):3897-907. doi: 10.1093/jxb/erw211


The calmodulin-like proteins AtCML4 and AtCML5 are single-pass membrane proteins targeted to the endomembrane system by an N-terminal signal anchor sequence

Ruge, R.; Flosdorff, S.; Ebersberger, I.; Chigri, F.; Vothknecht, U.;

J Exp Bot. 2016 Jun;67(13):3985-96. doi: 10.1093/jxb/erw101. Epub 2016 Mar 29.


An evolutionary view on thylakoid protein phosphorylation to uncover novel phosphorylation hotspots with potential functional implications

Grieco M.; Jain, A.; Ebersberger, I.; Teige, M.;

J Exp Bot. 2016 Jun;67(13):3883-96. doi: 10.1093/jxb/erw164. Epub 2016 Apr 25. Review.


2015 top

Acinetobacter equi sp. nov. isolated from horse faeces

Poppel, M.T.; Skiebe, E.; Laue, M.; Bergmann, H.; Ebersberger, I.; Garn, T.; Fruth, A.; Baumgardt, S.; Busse, H.J.; Wilharm, G.;

Int J Syst Evol Microbiol. 2015 Nov 30. doi: 10.1099/ijsem.0.000806


Acinetobacter baumannii Virulence Is Mediated by the Concerted Action of Three Phospholipases D

Stahl, J.; Bergmann, H.; Göttig, S.; Ebersberger, I.; Averhoff, B.;

PLoS One. 2015; 10(9): e0138360


Potential and pitfalls of eukaryotic metagenome skimming: A test case for lichens.

Greshake, B.; Zehr, S.; Dal Grande, F.; Meiser, A.; Schmitt, I.; Ebersberger, I.;

Mol Ecol Resour. 2015 Sep 8. doi: 10.1111/1755-0998.12463


The association of late-acting snoRNPs with human pre-ribosomal complexes requires the RNA helicase DDX21

Sloan, K. E.; Leisegang, M. S.; Doebele, C.; Ramírez, A. S.; Simm, S.; Safferthal, C.; Kretschmer, J.; Schorge, T.; Markoutsa, S.; Haag, S.; Karas, M.; Ebersberger, I.; Schleiff, E.; Watkins, N. J.; T. Bohnsack, M. T.

Nucl. Acids Res. (January 2015) 43 (1): 553-564


Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix

Feldmeyer, B.; Greshake, B.; Funke, E.; Patel, S.; Ebersberger, I.; Pfenninger, M.;

BMC Evolutionary Biology 2015, 15:164 doi:10.1186/s12862-015-0434-x


2014 top

Higher plant proteins of cyanobacterial origin - are they or are they not preferentially targeted to chloroplasts?

Bayer, R.G.; Köstler, T.; Jain, A.; Stael, S.; Ebersberger, I.; Teige, M.;

Mol Plant. 2014 Dec;7(12):1797-800.


A transcriptome approach to ecdysozoan phylogeny

Borner, J.; Rehm, P.; Schill, R. O.; Ebersberger, I.; Burmester, T.;

Mol Phylogenet Evol. 2014 Nov; 80:79-87


The evolution of the ribosome biogenesis pathway from a yeast perspective

Ebersberger, I.: Simm, S.; Leisegang, M. S.; Schmitzberger, P.; Mirus, O.; von Haeseler, A.; Bohnsack, M. T.; Schleiff, E.;

Nucl. Acids Res. 2014 42: 1509-1523


Transcriptome Data Reveal Syndermatan Relationships and Suggest the Evolution of Endoparasitism in Acanthocephala via an Epizoic Stage

Wey-Fabrizius, A. R.; Herlyn, H.; Rieger, B.; Rosenkranz, D.; Witek, A.; Welch, D. B. M. ; Ebersberger, I.; Hankeln, T.;

PLOS ONE February 10, 2014; DOI: 10.1371/journal.pone.0088618


2013 top

New phylogenomic data support the monophyly of Lophophorata and an Ectoproct-Phoronid clade and indicate that Polyzoa and Kryptrochozoa are caused by systematic bias

Nesnidal, M. P.; Helmkampf, M.; Meyer, A.; Witek, A.; Bruchhaus, I.; Ebersberger, I.; Hankeln, T.; Lieb, B.; Struck, T.H. and Hausdorf, B.;

BMC Evolutionary Biology.2013, 13:253; DOI: 10.1186/10.1186/1471-2148-13-253


Decisive Datasets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects

Dell'Ampio, E.; Meusemann, K.; Szucsich, N. U.; Peters, R. S.; Meyer, B.; Borner, J.; Petersen, M.; Aberer, A. J. ; Stamatakis, A.; Walzl, M. G.; Minh, B. Q.; von Haeseler, A.; Ebersberger, I.; Pass, G.; Misof, B.;

Mol Biol Evol 2013; DOI: 10.1093/molbev/mst196


Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and othereukaryotes for analysis of environmental sequencingdata

Bengtsson-Palme, J., Ryberg, M.; Hartmann, M.; Branco, S.; Wang, Z.; Godhe, A.; dee Wit, P.; Sánchez-García, M.; Ebersberger, I.; de Sousa, F.; Amend, A.; Jumpponen, A.; Unterseher, M.; Kristiansson, E.; Abarenkov, K.; Bertrand, Y.; Sanli, K.; Eriksson, K. M.; Vik, U.; Veldre, V.; Nilsson, R. H.

Methods in Ecology and Evolution 2013; DOI: 10.1111/2041-210X.12073


2012 top

REvolver: Modeling sequence evolution under domain constraints.

Koestler, T.; von Haeseler, A.; Ebersberger, I.;

Mol Biol Evol 2012; 29(9):2133-45


A Consistent Backbone for the Fungi.

Ebersberger, I.; de Matos Simoes, R.; Kupczok, A.; Gube, M.; Kothe, E.; Voigt, K.; von Haeseler, A.;

Mol Biol Evol 2012; 29:1319-1334.


Pancrustacean phylogeny in the light of new phylogenomic data: support for Remipedia as the possible sister group of Hexapoda.

von Reumont, BM.; Jenner, RA.; Wills, MA.; DellAmpio, E.; Pass, G.; Ebersberger, I.; Meyer, B.; Koenemann, S.; Iliffe, TM.; Stamatakis, A.; Niehuis, O.; Meusemann, K.; Misof, B.;

Mol Biol Evol 2012; 29:1031-1045


Review:    

The plant heat stress transcription factor (Hsf) family: structure, function and evolution.

Scharf, KD.; Berberich, T.; Ebersberger, I. and Nover, L.;

BBA - Gene Regulatory Mechanisms. 2012; 1819(2):104-19


2011 top

Phylogenomic analyses of malaria parasites and evolution of their exported proteins.

Pick, C.; Ebersberger, I.; Spielmann, T.; Bruchhaus, I. and Burmester, T.;

BMC Evolutionary Biology. 2011; 11:167


Zygomycetes, microsporidia, and the evolutionary ancestry of sex determination.

Koestler, T.; Ebersberger, I.;

Genome Biology and Evolution. 2011; 3:186-194


2010 top

FACT: Functional annotation transfer between proteins with similar feature architecture.

Koestler, T.; von Haeseler, A.; Ebersberger, I.;

BMC Bioinformatics. 2010; 11:417


A phylogenomic approach to resolve the arthropod tree of life.

Meusemann, K.; von Reumont, BM.; Simon, S.; Roeding, F.; Strauss, S.; Kück, P.; Ebersberger, I.; Walzl, M.; Pass, G.; Breuers, S.; Achter, V.; von Haeseler, A.; Burmester, T.; Hadrys, H.; Wägele, JW.; Misof, B.;

Mol Biol Evol. 2010; 27(11):2451-2464


2009 top

Support for the monophyletic origin of Gnathifera from phylogenomics.

Witek, A.; Herlyn, H.; Ebersberger, I.; Mark Welch, DB.; Hankeln, T.;

Mol Phylogenet Evol. 2009; 53(3):1037-1041


HaMStR: profile hidden markov model based search for orthologs in ESTs.

Ebersberger, I.; Strauss, S.; von Haeseler, A.;

BMC Evol Biol. 2009; 9:157


Genome-wide RNAi screen identifies genes involved in intestinal pathogenic bacterial infection.

Cronin, SJ.; Nehme, NT.; Limmer, S.; Liegeois, S.; Pospisilik, JA.; Schramek, D.; Leibbrandt, A.; Simoes Rde, M.; Gruber, S.; Puc, U.; Ebersberger, I.; Zoranovic, T.; Neely, GG.; von Haeseler, A.; Ferrandon, D.; Penninger, JM.;

Science. 2009; 325(5938):340-343


2008 top

Centrin4 coordinates cell and nuclear division in T. brucei.

Shi, J.; Franklin, JB.; Yelinek, JT.; Ebersberger, I.; Warren, G.; He, CY;.

J Cell Sci. 2008; 121(Pt 18):3062-3070


Rooted triple consensus and anomalous gene trees.

Ewing, GB.; Ebersberger, I.; Schmidt, HA.; von Haeseler, A.;

BMC Evol Biol. 2008; 8:118


TbG63, a golgin involved in Golgi architecture in Trypanosoma brucei.

Ramirez, IB.; de Graffenried, CL.; Ebersberger, I.; Yelinek, J.; He, CY.; Price, A.; Warren, G.;

J Cell Sci. 2008; 121(Pt 9):1538-1546


2007 top

Targeted deletion of AIF decreases mitochondrial oxidative phosphorylation and protects from obesity and diabetes.

Pospisilik, JA.; Knauf, C.; Joza, N.; Benit, P.; Orthofer, M.; Cani, PD.; Ebersberger, I.; Nakashima, T.; Sarao, R.; Neely, G.; Esterbauer, H.; Kozlov, A.; Kahn, CR.; Kroemer, G.; Rustin, P.; Burcelin, R.; Penninger, JM.;

Cell. 2007; 131(3):476-491


EST sequencing of Onychophora and phylogenomic analysis of Metazoa.

Roeding, F.; Hagner-Holler, S.; Ruhberg, H.; Ebersberger, I.; von Haeseler, A.; Kube, M.; Reinhardt, R.; Burmester, T.;

Mol Phylogenet Evol. 2007; 45(3):942-951


Mapping human genetic ancestry.

Ebersberger, I.; Galgoczy, P.; Taudien, S.; Taenzer, S.; Platzer, M.; von Haeseler, A.;

Mol Biol Evol. 2007; 24(10):2266-2276


2006 top

Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae.

Krause, J.; Dear, PH.; Pollack, JL.; Slatkin, M.; Spriggs, H.; Barnes, I.; Lister, AM.; Ebersberger, I.; Pääbo, S.; Hofreiter, M.;

Nature. 2006; 439(7077):724-727


Review:    

Should the draft chimpanzee sequence be finished?

Taudien, S.; Ebersberger, I.; Glöckner, G.; Platzer, M.;

Trends Genet. 2006; 22(3):122-125


2005 top

Cracks in the shell–zooming in on eggshell formation in the human parasite Schistosoma mansoni.

Ebersberger, I.; Knobloch, J.; Kunz, W.;

Dev Genes Evol. 2005; 215(5):261-267


A genomic region evolving toward different GC contents in humans and chimpanzees indicates a recent and regionally limited shift in the mutation pattern.

Ebersberger, I.; Meyer, M.;

Mol Biol Evol. 2005; 22(5):1240-1245


2003 top

A neutral explanation for the correlation of diversity with recombination rates in humans.

Hellmann, I.; Ebersberger, I.; Ptak, SE.; Płłbo, S.; Przeworski, M.;

Am J Hum Genet. 2003 Jun;72(6):1527-1535


Selection on human genes as revealed by comparisons to chimpanzee cDNA.

Hellmann, I.; Zollner, S.; Enard, W.; Ebersberger, I.; Nickel, B.; Paabo, S.;

Genome Res. 2003; 13(5):831-837


2002 top

Genomewide comparison of DNA sequences between humans and chimpanzees.

Ebersberger, I.; Metzler, D.; Schwarz, C.; Pääbo, S.;

Am J Hum Genet. 2002; 70(6):1490-1497


1997 top

A variable intron distribution in globin genes of Chironomus: evidence for recent intron gain.

Hankeln, T.; Friedl, H.; Ebersberger, I.; Martin, J.; Schmidt, ER.;

Gene. 1997; 205(1-2):151-160